I have recently ran into this problem of the missing assignment counter not counting all missing assignments through both my view (teacher) , students, and observers. Under a particular student's grade page, it gives you a total missing at the top, but if you take the time to scroll down, students have way more assignments tagged as missing that aren't being counted.
As a parent, if I saw " 0 missing assignments" I wouldn't take the time to scroll down to make sure that number was correct.
Example attached of a student who Canvas counts as missing 4 assignments but is actually missing 9 assignments.